If I connect Moodle Server A to Server B and have two users each with a user with the same exact user name (example jdoe), how does moodle resolve those when roaming to different servers using MNet?
Server A and Server B each have an entry in the remote Moodle's mdl_mnet_host table. The remote Moodle stores the id of the originating host for each user in the mdl_user table, so that each user record is associated with the correct originating server.
so there shouldn't be any problems if I have two identical user names on two servers then. correct?
correct. (Unless you have some code on your site (plugins, etc.) that only looks at the username, and not the originating host ID, but that kind of code should be very rare, since most code should be using the user id, and not the username.)